Variant report

Variant	rs564577
Chromosome Location	chr19:39926057-39926058
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10412931	0.85[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs10423537	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10424217	0.86[EUR][1000 genomes]
rs1110627	0.89[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs1130180	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12609112	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12978920	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12978954	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12979605	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12983040	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1529732	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1560730	0.85[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17626	1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs17628	0.90[ASN][1000 genomes]
rs1865091	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1865092	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1932	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2009970	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2060270	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2060271	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2060272	0.81[EUR][1000 genomes]
rs2116932	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2288933	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2288934	0.85[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2304219	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2304221	0.89[EUR][1000 genomes]
rs2353678	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2353679	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs251855	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs251856	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs251857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs251858	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs251859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs251860	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28528765	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28637729	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28649498	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs31725	0.85[GIH][hapmap]
rs31726	0.82[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs31727	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs31728	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34918990	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35647910	0.88[EUR][1000 genomes]
rs4390710	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802026	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803237	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803240	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803241	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803242	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4803245	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs4803246	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs4803247	0.96[CEU][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs480595	0.90[ASN][1000 genomes]
rs480656	0.90[ASN][1000 genomes]
rs481421	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs504017	0.83[ASN][1000 genomes]
rs530411	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[ASN][1000 genomes]
rs566130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59007555	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs640000	0.90[ASN][1000 genomes]
rs6508862	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6508863	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6508864	0.87[EUR][1000 genomes]
rs6508865	0.85[EUR][1000 genomes]
rs651601	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs686956	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7251384	0.87[EUR][1000 genomes]
rs7251652	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7255253	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7257526	0.87[MEX][hapmap];0.82[TSI][hapmap]
rs73035416	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73549933	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8107194	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8107647	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8110134	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8110716	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8111260	0.87[EUR][1000 genomes]
rs878754	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
3	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs564577	NUMBL	cis	parietal	SCAN
rs564577	B3GNT8	cis	parietal	SCAN
rs564577	BCAM	cis	parietal	SCAN
rs564577	EXOSC5	cis	cerebellum	SCAN
rs564577	RPS16	cis	Heart Left Ventricle	GTEx
rs564577	RPS16	Cis_1M	lymphoblastoid	RTeQTL
rs564577	RPS16	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39923200-39926200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
2	chr19:39923600-39926600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr19:39923800-39926400	Transcr. at gene 5' and 3'	A549	lung
4	chr19:39924200-39926400	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr19:39924600-39926200	Transcr. at gene 5' and 3'	NHEK	skin
6	chr19:39924600-39926400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
7	chr19:39925000-39926600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
8	chr19:39925000-39926600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
9	chr19:39925000-39927200	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr19:39925200-39927000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:39925200-39927400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr19:39925400-39926200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr19:39925400-39926200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr19:39925400-39926200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:39925400-39926200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:39925400-39926200	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr19:39925400-39926200	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr19:39925400-39926200	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr19:39925400-39926400	Active TSS	Gastric	stomach
20	chr19:39925400-39926400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr19:39925400-39927000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:39925400-39927000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:39925400-39927200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr19:39925400-39927200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:39925400-39927200	Active TSS	Psoas Muscle	Psoas
26	chr19:39925400-39927200	Active TSS	Right Ventricle	heart
27	chr19:39925400-39927400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr19:39925400-39927600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:39925400-39927600	Active TSS	GM12878-XiMat	blood
30	chr19:39925600-39926200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:39925600-39926200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:39925600-39926200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr19:39925600-39926200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:39925600-39926200	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr19:39925600-39926200	Flanking Active TSS	Liver	Liver
36	chr19:39925600-39926200	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr19:39925600-39926200	Flanking Active TSS	Fetal Brain Female	brain
38	chr19:39925600-39926200	Flanking Active TSS	Placenta	Placenta
39	chr19:39925600-39926200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr19:39925600-39926400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr19:39925600-39926400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr19:39925600-39926400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:39925600-39927000	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr19:39925600-39927000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:39925600-39927000	Active TSS	Fetal Kidney	kidney
46	chr19:39925600-39927000	Active TSS	Hela-S3	cervix
47	chr19:39925600-39927000	Active TSS	NHDF-Ad	bronchial
48	chr19:39925600-39927200	Active TSS	HMEC	breast
49	chr19:39925600-39927400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:39925600-39927400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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